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Jason was tired because he had been jogging.

They had been talking for over an hour before Tony arrived.

--> in both sentences, a past perfect continuous is used, is it also possible to use a past perfect and why?
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It would be grammatical, but it would not exactly be idiomatic.

You could say " . . because he had jogged around the park ten times," but "he was tired because he had jogged" is not natural.

When you say "he had been jogging," you imply that he had completed a certain regimen.
"He had jogged" doesn't give us much of a picture.

The talking example is a little different, because prior context could possibly give some substance to the conversation. That is, they had been talking about X.

Otherwise, "they had talked" seems to lack substance.